diff --git a/modules/nextflow/psltools/convert/main.nf b/modules/nextflow/psltools/convert/main.nf
new file mode 100644
index 0000000..2b0a499
--- /dev/null
+++ b/modules/nextflow/psltools/convert/main.nf
@@ -0,0 +1,62 @@
+/*
+Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+Distributed under the terms of the Apache License, Version 2.0.
+*/
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    PSLTOOLS_CONVERT — Convert PSL to BED
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+process PSLTOOLS_CONVERT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        '' :
+        'ghcr.io/alejandrogzi/psltools:latest' }"
+
+    input:
+    tuple val(meta), path(psl)
+
+    output:
+    tuple val(meta), path("*.bed")       , optional: true, emit: bed
+    tuple val(meta), path("*.bed.gz")    , optional: true, emit: bed_gz
+    path "versions.yml"                  , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args      = task.ext.args ?: ''
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    def type      = task.ext.type ?: '12'
+    def gzip      = task.ext.gzip ? "--gzip" : ""
+    """
+    psltools convert \\
+        $args \\
+        $gzip \\
+        --psl $psl \\
+        --out ${prefix}.bed \\
+        --type $type
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        psltools: \$( psltools --version | sed 's/psltools //g' )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bed
+    touch ${prefix}.bed.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        psltools: \$( psltools --version | sed 's/psltools //g' )
+    END_VERSIONS
+    """
+}
diff --git a/modules/nextflow/psltools/filter/main.nf b/modules/nextflow/psltools/filter/main.nf
new file mode 100644
index 0000000..c9b4343
--- /dev/null
+++ b/modules/nextflow/psltools/filter/main.nf
@@ -0,0 +1,58 @@
+/*
+Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+Distributed under the terms of the Apache License, Version 2.0.
+*/
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    PSLTOOLS_FILTER — Filter PSL files by score, strand, or other criteria.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+process PSLTOOLS_FILTER {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        '' :
+        'ghcr.io/alejandrogzi/psltools:latest' }"
+
+    input:
+    tuple val(meta), path(psl)
+
+    output:
+    tuple val(meta), path("*.psl")       , optional: true, emit: psl
+    tuple val(meta), path("*.psl.gz")    , optional: true, emit: psl_gz
+    path "versions.yml"                  , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args      = task.ext.args ?: ''
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    """
+    psltools filter \\
+        $args \\
+        --psl $psl \\
+        --out-psl ${prefix}.filtered.psl
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        psltools: \$( psltools --version | sed 's/psltools //g' )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.psl
+    touch ${prefix}.psl.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        psltools: \$( psltools --version | sed 's/psltools //g' )
+    END_VERSIONS
+    """
+}
diff --git a/modules/nextflow/psltools/merge/main.nf b/modules/nextflow/psltools/merge/main.nf
new file mode 100644
index 0000000..f9ff5f7
--- /dev/null
+++ b/modules/nextflow/psltools/merge/main.nf
@@ -0,0 +1,60 @@
+/*
+Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+Distributed under the terms of the Apache License, Version 2.0.
+*/
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    PSLTOOLS_MERGE — Merge PSL files into a single PSL file.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+process PSLTOOLS_MERGE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        '' :
+        'ghcr.io/alejandrogzi/psltools:latest' }"
+
+    input:
+    tuple val(meta), path(psls)
+
+    output:
+    tuple val(meta), path("*.psl")       , optional: true, emit: psl
+    tuple val(meta), path("*.psl.gz")    , optional: true, emit: psl_gz
+    path "versions.yml"                  , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args      = task.ext.args ?: ''
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    """
+    ls *.psl > psl.list
+
+    psltools merge \\
+        $args \\
+        --file psl.list \\
+        --out-psl ${prefix}.merged.psl
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        psltools: \$( psltools --version | sed 's/psltools //g' )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.merged.psl
+    touch ${prefix}.merged.psl.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        psltools: \$( psltools --version | sed 's/psltools //g' )
+    END_VERSIONS
+    """
+}
diff --git a/modules/nextflow/psltools/score/main.nf b/modules/nextflow/psltools/score/main.nf
new file mode 100644
index 0000000..65bc7df
--- /dev/null
+++ b/modules/nextflow/psltools/score/main.nf
@@ -0,0 +1,58 @@
+/*
+Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+Distributed under the terms of the Apache License, Version 2.0.
+*/
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    PSLTOOLS_SCORE — Score PSL files by summing the values of the alignment scores.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+process PSLTOOLS_SCORE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        '' :
+        'ghcr.io/alejandrogzi/psltools:latest' }"
+
+    input:
+    tuple val(meta), path(psl)
+
+    output:
+    tuple val(meta), path("*.tsv")       , optional: true, emit: tsv
+    tuple val(meta), path("*.tsv.gz")    , optional: true, emit: tsv_gz
+    path "versions.yml"                  , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args      = task.ext.args ?: ''
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    """
+    psltools score \\
+        $args \\
+        --psl $psl \\
+        --out ${prefix}.scores.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        psltools: \$( psltools --version | sed 's/psltools //g' )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.tsv
+    touch ${prefix}.tsv.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        psltools: \$( psltools --version | sed 's/psltools //g' )
+    END_VERSIONS
+    """
+}
diff --git a/modules/nextflow/psltools/sort/main.nf b/modules/nextflow/psltools/sort/main.nf
new file mode 100644
index 0000000..ecde3e2
--- /dev/null
+++ b/modules/nextflow/psltools/sort/main.nf
@@ -0,0 +1,58 @@
+/*
+Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+Distributed under the terms of the Apache License, Version 2.0.
+*/
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    PSLTOOLS_SORT — Sort PSL files by chromosome, start, or other criteria.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+process PSLTOOLS_SORT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        '' :
+        'ghcr.io/alejandrogzi/psltools:latest' }"
+
+    input:
+    tuple val(meta), path(psl)
+
+    output:
+    tuple val(meta), path("*.psl")       , optional: true, emit: psl
+    tuple val(meta), path("*.psl.gz")    , optional: true, emit: psl_gz
+    path "versions.yml"                  , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args      = task.ext.args ?: ''
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    """
+    psltools sort \\
+        $args \\
+        --psl $psl \\
+        --out ${prefix}.scores.psl
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        psltools: \$( psltools --version | sed 's/psltools //g' )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.psl
+    touch ${prefix}.psl.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        psltools: \$( psltools --version | sed 's/psltools //g' )
+    END_VERSIONS
+    """
+}
diff --git a/modules/nextflow/psltools/split/main.nf b/modules/nextflow/psltools/split/main.nf
new file mode 100644
index 0000000..f0e2cdd
--- /dev/null
+++ b/modules/nextflow/psltools/split/main.nf
@@ -0,0 +1,58 @@
+/*
+Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+Distributed under the terms of the Apache License, Version 2.0.
+*/
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    PSLTOOLS_SPLIT — Split PSL files into multiple PSL files.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+process PSLTOOLS_SPLIT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        '' :
+        'ghcr.io/alejandrogzi/psltools:latest' }"
+
+    input:
+    tuple val(meta), path(psl)
+
+    output:
+    tuple val(meta), path("*.psl")       , optional: true, emit: psl
+    tuple val(meta), path("*.psl.gz")    , optional: true, emit: psl_gz
+    path "versions.yml"                  , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args      = task.ext.args ?: ''
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    """
+    psltools split \\
+        $args \\
+        --psl $psl \\
+        --out-prefix ${prefix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        psltools: \$( psltools --version | sed 's/psltools //g' )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.psl
+    touch ${prefix}.psl.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        psltools: \$( psltools --version | sed 's/psltools //g' )
+    END_VERSIONS
+    """
+}
diff --git a/modules/nextflow/psltools/stats/main.nf b/modules/nextflow/psltools/stats/main.nf
new file mode 100644
index 0000000..5bf896e
--- /dev/null
+++ b/modules/nextflow/psltools/stats/main.nf
@@ -0,0 +1,59 @@
+/*
+Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+Distributed under the terms of the Apache License, Version 2.0.
+*/
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    PSLTOOLS_STATS — Get statistics about PSL files.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+process PSLTOOLS_STATS {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        '' :
+        'ghcr.io/alejandrogzi/psltools:latest' }"
+
+    input:
+    tuple val(meta), path(psl)
+
+    output:
+    tuple val(meta), path("*.json")       , optional: true, emit: json
+    tuple val(meta), path("*.tsv")        , optional: true, emit: tsv
+    path "versions.yml"                   , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args      = task.ext.args ?: ''
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    def extension = args.contains("--json") ? ".json" : ".tsv"
+    """
+    psltools stats \\
+        $args \\
+        --psl $psl \\
+        > ${prefix}.stats$extension
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        psltools: \$( psltools --version | sed 's/psltools //g' )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.stats.tsv
+    touch ${prefix}.stats.json
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        psltools: \$( psltools --version | sed 's/psltools //g' )
+    END_VERSIONS
+    """
+}
diff --git a/modules/nextflow/psltools/swap/main.nf b/modules/nextflow/psltools/swap/main.nf
new file mode 100644
index 0000000..0ea72d2
--- /dev/null
+++ b/modules/nextflow/psltools/swap/main.nf
@@ -0,0 +1,59 @@
+/*
+Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+Distributed under the terms of the Apache License, Version 2.0.
+*/
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    PSLTOOLS_SWAP — Swap PSL files from reference to query.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+process PSLTOOLS_SWAP {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        '' :
+        'ghcr.io/alejandrogzi/psltools:latest' }"
+
+    input:
+    tuple val(meta), path(psl)
+
+    output:
+    tuple val(meta), path("*.psl")       , optional: true, emit: psl
+    tuple val(meta), path("*.psl.gz")    , optional: true, emit: psl_gz
+    path "versions.yml"                  , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args      = task.ext.args ?: ''
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    def extension = args.contains("--json") ? ".json" : ".tsv"
+    """
+    psltools stats \\
+        $args \\
+        --psl $psl \\
+        --out-psl ${prefix}.swapped.psl
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        psltools: \$( psltools --version | sed 's/psltools //g' )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.swapped.psl
+    touch ${prefix}.swapped.psl.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        psltools: \$( psltools --version | sed 's/psltools //g' )
+    END_VERSIONS
+    """
+}
diff --git a/modules/wdl/psltools/convert/main.wdl b/modules/wdl/psltools/convert/main.wdl
new file mode 100644
index 0000000..e721864
--- /dev/null
+++ b/modules/wdl/psltools/convert/main.wdl
@@ -0,0 +1,67 @@
+# Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+# Distributed under the terms of the Apache License, Version 2.0.
+
+# PSLTOOLS_CONVERT — Convert PSL to BED
+
+version 1.3
+
+task convert {
+  input {
+    File psl
+    String extra_args = ""
+    String prefix = ""
+    String type = "12"
+    Boolean gzip = false
+  }
+
+  String out_prefix = if prefix == "" then basename(psl, ".psl") else prefix
+
+  command <<<
+    set -euo pipefail
+
+    gzip_arg=""
+    if ~{gzip}; then
+      gzip_arg="--gzip"
+    fi
+
+    psltools convert \
+      ~{extra_args} \
+      $gzip_arg \
+      --psl ~{psl} \
+      --out ~{out_prefix}.bed \
+      --type ~{type}
+  >>>
+
+  output {
+    File bed = "~{out_prefix}.bed"
+    File? bed_gz = "~{out_prefix}.bed.gz"
+  }
+
+  requirements {
+    container: "ghcr.io/alejandrogzi/psltools:latest"
+  }
+}
+
+workflow run {
+  input {
+    File psl
+    String extra_args = ""
+    String prefix = ""
+    String type = "12"
+    Boolean gzip = false
+  }
+
+  call convert {
+    input:
+      psl = psl,
+      extra_args = extra_args,
+      prefix = prefix,
+      type = type,
+      gzip = gzip
+  }
+
+  output {
+    File bed = convert.bed
+    File? bed_gz = convert.bed_gz
+  }
+}
diff --git a/modules/wdl/psltools/filter/main.wdl b/modules/wdl/psltools/filter/main.wdl
new file mode 100644
index 0000000..9408f95
--- /dev/null
+++ b/modules/wdl/psltools/filter/main.wdl
@@ -0,0 +1,54 @@
+# Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+# Distributed under the terms of the Apache License, Version 2.0.
+
+# PSLTOOLS_FILTER — Filter PSL files by score, strand, or other criteria.
+
+version 1.3
+
+task filter {
+  input {
+    File psl
+    String extra_args = ""
+    String prefix = ""
+  }
+
+  String out_prefix = if prefix == "" then basename(psl, ".psl") else prefix
+
+  command <<<
+    set -euo pipefail
+
+    psltools filter \
+      ~{extra_args} \
+      --psl ~{psl} \
+      --out-psl ~{out_prefix}.filtered.psl
+  >>>
+
+  output {
+    File filtered_psl = "~{out_prefix}.filtered.psl"
+    File? filtered_psl_gz = "~{out_prefix}.filtered.psl.gz"
+  }
+
+  requirements {
+    container: "ghcr.io/alejandrogzi/psltools:latest"
+  }
+}
+
+workflow run {
+  input {
+    File psl
+    String extra_args = ""
+    String prefix = ""
+  }
+
+  call filter {
+    input:
+      psl = psl,
+      extra_args = extra_args,
+      prefix = prefix
+  }
+
+  output {
+    File filtered_psl = filter.filtered_psl
+    File? filtered_psl_gz = filter.filtered_psl_gz
+  }
+}
diff --git a/modules/wdl/psltools/merge/main.wdl b/modules/wdl/psltools/merge/main.wdl
new file mode 100644
index 0000000..f4dade0
--- /dev/null
+++ b/modules/wdl/psltools/merge/main.wdl
@@ -0,0 +1,54 @@
+# Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+# Distributed under the terms of the Apache License, Version 2.0.
+
+# PSLTOOLS_MERGE — Merge PSL files into a single PSL file.
+
+version 1.3
+
+task merge {
+  input {
+    Array[File] psls
+    String extra_args = ""
+    String prefix = "merged"
+  }
+
+  command <<<
+    set -euo pipefail
+
+    ls *.psl > psl.list
+
+    psltools merge \
+      ~{extra_args} \
+      --file psl.list \
+      --out-psl ~{prefix}.merged.psl
+  >>>
+
+  output {
+    File merged_psl = "~{prefix}.merged.psl"
+    File? merged_psl_gz = "~{prefix}.merged.psl.gz"
+  }
+
+  requirements {
+    container: "ghcr.io/alejandrogzi/psltools:latest"
+  }
+}
+
+workflow run {
+  input {
+    Array[File] psls
+    String extra_args = ""
+    String prefix = "merged"
+  }
+
+  call merge {
+    input:
+      psls = psls,
+      extra_args = extra_args,
+      prefix = prefix
+  }
+
+  output {
+    File merged_psl = merge.merged_psl
+    File? merged_psl_gz = merge.merged_psl_gz
+  }
+}
diff --git a/modules/wdl/psltools/score/main.wdl b/modules/wdl/psltools/score/main.wdl
new file mode 100644
index 0000000..7bdd8f8
--- /dev/null
+++ b/modules/wdl/psltools/score/main.wdl
@@ -0,0 +1,54 @@
+# Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+# Distributed under the terms of the Apache License, Version 2.0.
+
+# PSLTOOLS_SCORE — Score PSL files by summing the values of the alignment scores.
+
+version 1.3
+
+task score {
+  input {
+    File psl
+    String extra_args = ""
+    String prefix = ""
+  }
+
+  String out_prefix = if prefix == "" then basename(psl, ".psl") else prefix
+
+  command <<<
+    set -euo pipefail
+
+    psltools score \
+      ~{extra_args} \
+      --psl ~{psl} \
+      --out ~{out_prefix}.scores.tsv
+  >>>
+
+  output {
+    File scores_tsv = "~{out_prefix}.scores.tsv"
+    File? scores_tsv_gz = "~{out_prefix}.scores.tsv.gz"
+  }
+
+  requirements {
+    container: "ghcr.io/alejandrogzi/psltools:latest"
+  }
+}
+
+workflow run {
+  input {
+    File psl
+    String extra_args = ""
+    String prefix = ""
+  }
+
+  call score {
+    input:
+      psl = psl,
+      extra_args = extra_args,
+      prefix = prefix
+  }
+
+  output {
+    File scores_tsv = score.scores_tsv
+    File? scores_tsv_gz = score.scores_tsv_gz
+  }
+}
diff --git a/modules/wdl/psltools/sort/main.wdl b/modules/wdl/psltools/sort/main.wdl
new file mode 100644
index 0000000..ae9b493
--- /dev/null
+++ b/modules/wdl/psltools/sort/main.wdl
@@ -0,0 +1,54 @@
+# Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+# Distributed under the terms of the Apache License, Version 2.0.
+
+# PSLTOOLS_SORT — Sort PSL files by chromosome, start, or other criteria.
+
+version 1.3
+
+task sort {
+  input {
+    File psl
+    String extra_args = ""
+    String prefix = ""
+  }
+
+  String out_prefix = if prefix == "" then basename(psl, ".psl") else prefix
+
+  command <<<
+    set -euo pipefail
+
+    psltools score \
+      ~{extra_args} \
+      --psl ~{psl} \
+      --out ~{out_prefix}.scores.tsv
+  >>>
+
+  output {
+    File scores_tsv = "~{out_prefix}.scores.tsv"
+    File? scores_tsv_gz = "~{out_prefix}.scores.tsv.gz"
+  }
+
+  requirements {
+    container: "ghcr.io/alejandrogzi/psltools:latest"
+  }
+}
+
+workflow run {
+  input {
+    File psl
+    String extra_args = ""
+    String prefix = ""
+  }
+
+  call sort {
+    input:
+      psl = psl,
+      extra_args = extra_args,
+      prefix = prefix
+  }
+
+  output {
+    File scores_tsv = sort.scores_tsv
+    File? scores_tsv_gz = sort.scores_tsv_gz
+  }
+}
diff --git a/modules/wdl/psltools/split/main.wdl b/modules/wdl/psltools/split/main.wdl
new file mode 100644
index 0000000..c8c02db
--- /dev/null
+++ b/modules/wdl/psltools/split/main.wdl
@@ -0,0 +1,54 @@
+# Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+# Distributed under the terms of the Apache License, Version 2.0.
+
+# PSLTOOLS_SPLIT — Split PSL files into multiple PSL files.
+
+version 1.3
+
+task split {
+  input {
+    File psl
+    String extra_args = ""
+    String prefix = ""
+  }
+
+  String out_prefix = if prefix == "" then basename(psl, ".psl") else prefix
+
+  command <<<
+    set -euo pipefail
+
+    psltools split \
+      ~{extra_args} \
+      --psl ~{psl} \
+      --out-prefix ~{out_prefix}
+  >>>
+
+  output {
+    Array[File] psls = glob("*.psl")
+    Array[File] psls_gz = glob("*.psl.gz")
+  }
+
+  requirements {
+    container: "ghcr.io/alejandrogzi/psltools:latest"
+  }
+}
+
+workflow run {
+  input {
+    File psl
+    String extra_args = ""
+    String prefix = ""
+  }
+
+  call split {
+    input:
+      psl = psl,
+      extra_args = extra_args,
+      prefix = prefix
+  }
+
+  output {
+    Array[File] psls = split.psls
+    Array[File] psls_gz = split.psls_gz
+  }
+}
diff --git a/modules/wdl/psltools/stats/main.wdl b/modules/wdl/psltools/stats/main.wdl
new file mode 100644
index 0000000..9a76cd4
--- /dev/null
+++ b/modules/wdl/psltools/stats/main.wdl
@@ -0,0 +1,59 @@
+# Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+# Distributed under the terms of the Apache License, Version 2.0.
+
+# PSLTOOLS_STATS — Get statistics about PSL files.
+
+version 1.3
+
+task stats {
+  input {
+    File psl
+    String extra_args = ""
+    String prefix = ""
+  }
+
+  String out_prefix = if prefix == "" then basename(psl, ".psl") else prefix
+
+  command <<<
+    set -euo pipefail
+
+    extension=".tsv"
+    if [[ "~{extra_args}" == *"--json"* ]]; then
+      extension=".json"
+    fi
+
+    psltools stats \
+      ~{extra_args} \
+      --psl ~{psl} \
+      > ~{out_prefix}.stats$extension
+  >>>
+
+  output {
+    File? stats_json = "~{out_prefix}.stats.json"
+    File? stats_tsv = "~{out_prefix}.stats.tsv"
+  }
+
+  requirements {
+    container: "ghcr.io/alejandrogzi/psltools:latest"
+  }
+}
+
+workflow run {
+  input {
+    File psl
+    String extra_args = ""
+    String prefix = ""
+  }
+
+  call stats {
+    input:
+      psl = psl,
+      extra_args = extra_args,
+      prefix = prefix
+  }
+
+  output {
+    File? stats_json = stats.stats_json
+    File? stats_tsv = stats.stats_tsv
+  }
+}
diff --git a/modules/wdl/psltools/swap/main.wdl b/modules/wdl/psltools/swap/main.wdl
new file mode 100644
index 0000000..06fe715
--- /dev/null
+++ b/modules/wdl/psltools/swap/main.wdl
@@ -0,0 +1,54 @@
+# Copyright (c) 2026 The Hiller Lab at the Senckenberg Gessellschaft für Naturforschung
+# Distributed under the terms of the Apache License, Version 2.0.
+
+# PSLTOOLS_SWAP — Swap PSL files from reference to query.
+
+version 1.3
+
+task swap {
+  input {
+    File psl
+    String extra_args = ""
+    String prefix = ""
+  }
+
+  String out_prefix = if prefix == "" then basename(psl, ".psl") else prefix
+
+  command <<<
+    set -euo pipefail
+
+    psltools swap \
+      ~{extra_args} \
+      --psl ~{psl} \
+      --out-psl ~{out_prefix}.swapped.psl
+  >>>
+
+  output {
+    File swapped_psl = "~{out_prefix}.swapped.psl"
+    File? swapped_psl_gz = "~{out_prefix}.swapped.psl.gz"
+  }
+
+  requirements {
+    container: "ghcr.io/alejandrogzi/psltools:latest"
+  }
+}
+
+workflow run {
+  input {
+    File psl
+    String extra_args = ""
+    String prefix = ""
+  }
+
+  call swap {
+    input:
+      psl = psl,
+      extra_args = extra_args,
+      prefix = prefix
+  }
+
+  output {
+    File swapped_psl = swap.swapped_psl
+    File? swapped_psl_gz = swap.swapped_psl_gz
+  }
+}